X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=blobdiff_plain;f=alg%2Fmussa.cpp;h=82b1d4a6585e49c1a946e9093413b0be357ab570;hp=f75290c58705c68ea8e7ccb152da253fde976cbb;hb=02adcab9918657891638e68580b8b88e6d935875;hpb=7d16486e23b3d94c49986b082b9de1b508fd6183

diff --git a/alg/mussa.cpp b/alg/mussa.cpp
index f75290c..82b1d4a 100644
--- a/alg/mussa.cpp
+++ b/alg/mussa.cpp
@@ -639,6 +639,10 @@ Mussa::load(fs::path ana_file)
   vector<FLPs> empty_FLP_vector;
   FLPs dummy_comp;
 
+
+  //--------------------------------------------------------
+  // Load Muway
+  //--------------------------------------------------------
   analysis_path = ana_file;
   analysis_name = ana_path.leaf();
   fs::path muway(analysis_name+".muway", fs::native);
@@ -650,24 +654,63 @@ Mussa::load(fs::path ana_file)
   threshold = the_paths.get_threshold();
   soft_thres = threshold;
 
-  int seq_num = the_paths.sequence_count();
+
+  //--------------------------------------------------------
+  // Load Sequence
+  //--------------------------------------------------------
+  //int seq_num = the_paths.sequence_count();
 
   fs::path museq(analysis_name + ".museq", fs::native);
   a_file_path = analysis_path / museq;
 
   // this is a bit of a hack due to C++ not acting like it should with files
-  for (i = 1; i <= seq_num; i++)
+  /*for (i = 1; i <= seq_num; i++)
   {
     boost::shared_ptr<Sequence> tmp_seq(new Sequence);
     tmp_seq->load_museq(a_file_path, i);
     the_seqs.push_back(tmp_seq);
+  }*/
+  
+  i = 1;
+  //int seq_num = 0;
+  boost::filesystem::fstream load_museq_fs;
+  load_museq_fs.open(a_file_path, std::ios::in);
+  boost::shared_ptr<Sequence> tmp_seq;
+  while (1)
+  {
+    tmp_seq = Sequence::load_museq(load_museq_fs);
+    
+    if (tmp_seq)
+    {
+      the_seqs.push_back(tmp_seq);
+    }
+    else
+    {
+      break;
+    }
+    
+    
+    //safe guard in case of an infinate loop.
+    //FIXME: If mussa can handle a comparison of 10000 sequences
+    // in the future, then this code should be fixed.
+    if (i == 10000)
+    {
+      throw mussa_load_error(" Run away sequence load!");
+    }
+    i++;
   }
+  load_museq_fs.close();
   
+  //--------------------------------------------------------
+  // Load Motifs
+  //--------------------------------------------------------
   fs::path mtl(analysis_name + ".mtl", fs::native);
   fs::path motif_file = analysis_path / mtl;
   if (fs::exists(motif_file)) {
     load_motifs(motif_file);
   }
+  
+  vector<Sequence>::size_type seq_num = the_seqs.size();
   empty_FLP_vector.clear();
   for(i = 0; i < seq_num; i++)
   {
@@ -676,6 +719,7 @@ Mussa::load(fs::path ana_file)
       all_comps[i].push_back(dummy_comp);
   }
   
+  
   for(i = 0; i < seq_num; i++)
   {
     for(i2 = i+1; i2 < seq_num; i2++)